Biology subjects

Luebke-Becker, A.

Publications and source records attributed to Luebke-Becker, A..

3 recordsLinked to original sources

bioRxiv2025

Phylodynamics and genome-wide association studies reveal the expansion of modern Streptococcus canis in Germany

Streptoccocus canis is a leading canine pathogen causing 22.4% of canine streptococcal infections. However, knowledge of factors contributing to S. canis expansion is limited. This study uses population genetics to structure a S. canis dataset of 585 isolates and identify genetic markers contributing to the success of each dominant lineage. The dataset is composed of canine, feline and bovine isolates primarily from Germany collected between the years 1996 and 2021. We performed Multi-Locus Sequence Typing (MLST) for an initial analysis and clustered the population with fastBAPS based on the whole genome. Dated phylogenies were inferred with BEAST and Genome-Wide Association Studies (GWAS) were conducted with Scoary. MLST showed that in Germany there are two dominant groups of canine S. canis, ST43 (n= 75) and ST9 (n= 51), which were grouped into BAPS-6 and BAPS-5, respectively. The BAPS-6 cluster emerged as early as 1988 with major expansion starting around 2010. We showed via GWAS that this cluster is associated with a putative Streptococcus anginosus derived integrative and conjugative element carrying a putative cysteine protease. Furthermore, the BAPS-5 cluster emerged around 1786 with a bovine/feline subcluster appearing around 1879. This subcluster is associated with a variant of the streptococcal lac operon, which appears to have resulted from an exchange with Streptococcus dysgalactiae. We present the largest population genetics study to date for S. canis where we show that its expansion is associated with genetic exchange with other streptococcal species leading to increased pathogenic potential (BAPS-6) or host adaptation (BAPS-5). ImportanceStreptococcus canis is a bacterium which poses considerable threat to the health of dogs through superficial infections. Current research could benefit from understanding the reasons for its expansion and spread into other hosts. We looked at the genomes of 585 S. canis isolates collected during a 25-year period and identified which parts of the population were the most successful. With powerful statistical methods, we found that two groups of S. canis were the most effective: a canine group which had become more pathogenic by acquiring DNA from Streptococcus anginosus, and another group which spread from dogs into cats and cows by acquiring genetic material for lactose consumption from Streptococcus dysgalactiae. For the first time, we link the expansion of major S. canis groups to genetic exchange events with closely related streptococcal species to understand S. canis evolution and spread.

microbiology↗

bioRxiv2024

On the ecology of Acinetobacter baumannii - jet stream rider and opportunist by nature

The natural reservoirs of the nosocomial pathogen Acinetobacter baumannii are not well defined. We previously identified white storks as a model system to study the ecology of A. baumannii. Having screened more than 1,300 white stork nestlings over a period of six years across different regions of Poland and Germany (overall isolation rate of [~]29.5%), including food chain analyses and environmental samplings, we come up with a detailed picture of the dynamics and diversity of A. baumannii in their natural habitats. Adult storks, rather than being stably colonized with strains of A. baumannii which are successively transferred to their offspring, instead initially encounter these bacteria while foraging. Among their common food sources, consisting of earthworms, small mammals, and insects, we identified earthworms as a potential source of A. baumannii, but more so the associated soil as well as plant roots. Through this, hotspot soil and compost habitats were identified which enable population dynamics to be studied over the course of the year. We demonstrate that sterilized plant material is rapidly colonized by airborne A. baumannii suggesting they patrol to search for novel habitats, being opportunist by nature. The prevalence of A. baumannii exhibited a strong seasonality and peaked during summer. The strains we collected in Poland and Germany represent more than 50% of the worldwide known diversity in terms of the intrinsic OXA-51-like {beta}-lactamase. A set of [~]400 genomes was determined and compared to a diverse set of publicly available genomes. Our pan-genome estimate of the species ([~]51,000 unique genes) more than doubles the amount proposed by previous studies. Core-genome based phylogenetic analyses illustrated numerous links between wildlife isolates and hospital strains, including ancient as well as recent intercontinental transfer. Our data further suggest massive radiation within the species early after its emergence, matching with human activity during the Neolithic. Deforestation in particular seemed to set the stage for this bloom as we found that forests do not provide conducive conditions for the proliferation of A. baumannii. In contrast, wet and nutrient-rich soil alongside rivers sampled during the summer can yield an isolation rate of [~]30%. Linking published work on the interaction between A. baumannii and fungi and on aspergillosis as a major cause of mortality in white stork nestlings to our findings, we hypothesized that fungi and A. baumannii share a long history of coevolution. Interaction studies revealed the capability of A. baumannii to adhere to fungal spores and to suppress spore germination. Taken together, the intrinsic resistance endowment and potential to acquire antibiotic resistance can be explained by coevolution with antibiotic-producing fungi and other microorganisms within soil, and resistance to desiccation stress and radiation can be interpreted in the light of intercontinental hitchhiking through fungal spores. Originality - SignificanceThe ecology of the nosocomial pathogen Acinetobacter baumannii remains poorly understood outside the hospital. Here, we present the most comprehensive study on its environmental biology to date, after having collected more than 1,450 independent isolates of which around 400 were whole genome-sequenced. This study more than doubles the size of the pan-genome of the species, illustrating both the diversity of our collection and the bias of previous work, but also the bottleneck for the establishment of lineages within the hospital environment. We reached isolation rates of about 30% both in white stork (Ciconia ciconia) nestlings and in soil samples when considering for sampling all preferences of A. baumannii we uncovered. Thus, it is now possible to study the ecology and evolution of A. baumannii in nature at an unprecedented temporal and spatial resolution. We describe the worldwide spread of A. baumannii lineages in nature as an ancient phenomenon that even surpasses that of human-associated bacteria in magnitude. This is likely due to airborne spread, putatively facilitated by association with fungal spores. We propose that A. baumannii is an opportunist by nature, using airborne patrolling to rapidly enter new suitable habitats consisting of organic matter in early stages of decomposition. Our collective data suggest that A. baumannii, early after its speciation, went through massive radiation during the Neolithic, likely due to deforestation, settlement and farming producing numerous favorable habitats. Their natural lifestyle, which requires rapid adaptability to various habitats as well as tolerance to desiccation, radiation and antibiotic stress, perfectly predispose these opportunistic pathogens to establish within the hospital setting. Comparison of genomes from environmental and clinical isolates will now enable studies of the adaptive evolution of environmental bacteria towards multidrug-resistant opportunistic pathogens.

microbiology↗

bioRxiv2023

Antibiotic prophylaxis and hospitalization of horses subjected to median laparotomy: gut microbiota trajectories and abundance increase of Escherichia

Horse clinics are hotspots for the accumulation and spread of clinically relevant and zoonotic multidrug-resistant bacteria, including extended-spectrum {beta}-lactamase producing (ESBL) Enterobacterales. Although median laparotomy in cases of acute equine colic is a frequently performed surgical intervention, knowledge about the effects of peri-operative antibiotic prophylaxis (PAP) based on a combination of penicillin and gentamicin on the gut microbiota is limited. Therefore, we collected fecal samples of horses from a non-hospitalized control group (CG) and from horses receiving either a pre-surgical single-shot (SSG) or a peri-operative 5-day (5DG) course of PAP. To assess differences between the two PAP regimens and the CG, all samples obtained at hospital admission (t0), on days three (t1) and ten (t2) after surgery, were screened for ESBL-producing Enterobacterales and subjected to 16S rRNA V1- V2 gene sequencing. We included 48 samples in the SSG (n=16 horses), 45 in the 5DG (n=15) and 20 in the CG (n=10). Two samples (6.5%) were positive for ESBL-producing Enterobacterales at t0 while this rate increased to 67% at t1 and decreased only slightly at t2 (61%). Shannon diversity index (SDI) was used to evaluate alpha-diversity changes, revealing that horses suffering from acute colic seemed to have a compromised fecal microbiota composition (5DG, SDImean of 5.90; SSG, SDImean of 6.17) when compared to the CG (SDImean of 6.53) at t0, although the difference lacked significance. Alpha-diversity decreased significantly in both PAP groups at t1, while at t2 the onset of microbiome recovery was noticed. Although we did not identify a significant SDImean difference with respect to PAP duration, the community structure (beta-diversity) was considerably restricted in samples of the 5DG at t1, most likely due to the ongoing administration of antibiotics. An increased abundance of Enterobacteriaceae, especially Escherichia, was noted for both study groups at t1. Further studies are needed to reveal important factors promoting the increase and residency of ESBL-producing Enterobacterales among hospitalized horses.

microbiology↗